r - Clean bad data automatically

To convert a factor to numeric, you need to convert to character first:

no2<-factor(c(5,4,"c1",54,"c5",seq(2:50)))
no2_num <- as.numeric(as.character(no2)) 
#Warning message:
#  NAs introduced by coercion 
no2_clean <- na.omit(no2_num) #remove NAs resulting from the bad data

# [1]  5  4 54  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
# [40] 37 38 39 40 41 42 43 44 45 46 47 48 49
# attr(,"na.action")

# [1] 3 5
# attr(,"class")
# [1] "omit"

length(attr(no2_clean,"na.action"))/length(no2)*100
#[1] 3.703704